Question: rna-seq fastqc number of parameters to pass
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falkjlkdfsnddf • 0 wrote:
Can i use the RNA seq data, which has passed only a few FASTQC parameters for data analysis.
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modified 5.0 years ago
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Biostar ♦♦ 20
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5.2 years ago by
falkjlkdfsnddf • 0
Err... First, I think you should write again the question and try to explain it in a clearer way. Second, what do you mean by "only a few FASTQC parameters"? Some of the parameters are "more essential" than others depending on your downstream analysis or experiment goal. Of course you can use the data with bad quality.. but, obviously the results will be affected.
Just to add to what airan said, some of the fastQC tests are meaningless for RNAseq data, while others are important. Without knowing which ones didn't pass and what the associated graphs look like we can't give you any advise.
Perhaps you want to read fastqc documentation here (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and choose yourself the parameters. It is explained in a very easy and clear way. Furthermore, there are nice examples of good and bad quality data. If I needed to choose "most important" parameter to pass, I would go for "Overrepresented sequences" and "Per base sequence quality". But I repeat, this depends strongly on your data, your experiment, your downstream analysis...